[lammps-users] Identify Atom ID of all atoms of functional group.

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1

Hello LAMMPS users,

I am using LAMMPS window version 19 March 2020. I did molecular modelling using Material Studio then I converted to LAMMPSDATA.format. I am using pcff force field.

I have some functional group which have covalent bonding with graphene on one side and epoxy on other side. I want to find the VACF of functional groups.Lets say if I have a functional group i.e., a benzene ring with single amine. Is there any command in LAMMPS which can do first matching with functional group (a benzne ring with a nitrogen). This would identify all atoms with similar structure. Then somehow I can extract Atom ID of all atoms.

Thanks and regards,
Ankit

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LAMMPS has no concept of chemistry and functional groups or similar. So any kind of labeling need to be done by you and explicitly. The most common approach is to change the molecule ID for atoms that should be identified in a particular way in the data file already. Then this property/value can be used to identify and group atoms from within LAMMPS.
Another option would be creating atomfile variables with files that set a value to non-zero for selected atoms and then use that property to group them for further analysis.

Axel.